Police said the man targeted young girls at a dozen centers in Australia and overseas for 15 years.
He was arrested in August 2022, but it took a year for the police to investigate and identify the victims.
Officials say it is one of the most "horrific" cases they have seen so far.
The 45-year-old man faces 246 charges of rape and 673 charges of indecent assault against children, most of which are in aggravated conditions.
The most serious charges carry a maximum life sentence.
Additionally, he faces hundreds of charges of filming and distributing child abuse materials.
Police claim to have recorded all of his abuse and say they found 4,000 images and videos on his electronic devices.
The alleged offenses occurred at ten childcare centers in Queensland, one childcare center in New South Wales, and an unnamed overseas country.
